Hi Alex, Is the search non-specific or there the correct peptides are not expected to conform to any enzymatic rules? If it is the latter you should disable the NTT and NMC models in the TPP, since correct peptides are not any more likely to have certain ends than the incorrect peptides. If it is the former then you should specify the enzyme when you run InteractParser and that way the NTT and NMC info will be recorded in the interact.pep.xml file despite the search being nonspecific. Does that make sense?
-David On Fri, Mar 26, 2010 at 6:12 AM, Alex <[email protected]> wrote: > Hi All, > > I'd like to have some opinions on how to validate a dataset with > no_enzyme specificty using PeptideProphet ? > > Until now it looks like it's difficult to get a model working. I > converted to pepxml using -Enonspecific from Mascot or Sequest by it > looks like the model has difficulty. I'm wondering who has experience > with nonspecific samples and validation. Should I turn off some > standard features like -OFNM ??? > > Thanks for any help. > > Alex > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
